ENST00000462876.5:n.1007-2570A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000462876.5(CAV2):n.1007-2570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,170 control chromosomes in the GnomAD database, including 967 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.10 ( 967 hom., cov: 32)
Consequence
CAV2
ENST00000462876.5 intron
ENST00000462876.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.938
Publications
7 publications found
Genes affected
CAV2 (HGNC:1528): (caveolin 2) The protein encoded by this gene is a major component of the inner surface of caveolae, small invaginations of the plasma membrane, and is involved in essential cellular functions, including signal transduction, lipid metabolism, cellular growth control and apoptosis. This protein may function as a tumor suppressor. This gene and related family member (CAV1) are located next to each other on chromosome 7, and express colocalizing proteins that form a stable hetero-oligomeric complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. Additional isoforms resulting from the use of alternate in-frame translation initiation codons have also been described, and shown to have preferential localization in the cell (PMID:11238462). [provided by RefSeq, May 2011]
CAV2 Gene-Disease associations (from GenCC):
- amyotrophic lateral sclerosisInheritance: AD Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAV2-DT | NR_188009.1 | n.163+4155T>C | intron_variant | Intron 1 of 3 | ||||
CAV2-DT | NR_188010.1 | n.163+4155T>C | intron_variant | Intron 1 of 3 | ||||
CAV2-DT | NR_188011.1 | n.163+4155T>C | intron_variant | Intron 1 of 4 | ||||
CAV2-DT | NR_188012.1 | n.163+4155T>C | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.102 AC: 15460AN: 152052Hom.: 961 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
15460
AN:
152052
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.102 AC: 15488AN: 152170Hom.: 967 Cov.: 32 AF XY: 0.0976 AC XY: 7263AN XY: 74420 show subpopulations
GnomAD4 genome
AF:
AC:
15488
AN:
152170
Hom.:
Cov.:
32
AF XY:
AC XY:
7263
AN XY:
74420
show subpopulations
African (AFR)
AF:
AC:
7253
AN:
41486
American (AMR)
AF:
AC:
1035
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
312
AN:
3468
East Asian (EAS)
AF:
AC:
3
AN:
5176
South Asian (SAS)
AF:
AC:
102
AN:
4830
European-Finnish (FIN)
AF:
AC:
690
AN:
10614
Middle Eastern (MID)
AF:
AC:
19
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5740
AN:
68014
Other (OTH)
AF:
AC:
215
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
710
1421
2131
2842
3552
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
156
312
468
624
780
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
57
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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